This page displays a compiled list of yeast transcription factor resources. Included are data on transcription factor target genes and transcription factor regulatory networks in yeast, links to web servers providing easy-to-use TF searches and other potentially helpful resources. I also added notes about what data I have gotten from each dataset for the Cin5p targets list.

//[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4JW10XT-1&_user=945462&_coverDate=06%2F30%2F2006&_rdoc=22&_fmt=high&_orig=browse&_srch=doc-info(%23toc%236899%232006%23996399998%23626365%23FLA%23display%23Volume)&_cdi=6899&_sort=d&_docanchor=&_ct=23&_acct=C000048964&_version=1&_urlVersion=0&_userid=945462&md5=b67d2bfd6d27c7704eece1bbc163f1e6 Full text from ScienceDirect]

//[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4JW10XT-1&_user=945462&_coverDate=06%2F30%2F2006&_rdoc=22&_fmt=high&_orig=browse&_srch=doc-info(%23toc%236899%232006%23996399998%23626365%23FLA%23display%23Volume)&_cdi=6899&_sort=d&_docanchor=&_ct=23&_acct=C000048964&_version=1&_urlVersion=0&_userid=945462&md5=b67d2bfd6d27c7704eece1bbc163f1e6 Full text from ScienceDirect]

Used new algoithm to construct temporal networks of yeast's response to various stresses, including cold shock. For cold shock data, the paper analyzes data from the Gasch, ''et al.'' (2000) paper. Supplementary data has cold shock temporal response, but does not show any interactions between transcription factors and targets. (Note: the Gasch et al. paper does not have a true "cold shock" response. They only measure the effect of a temperature downshift from 37°C to 25°C. Cold shock is defined in the range of 10°C to 18°C

** The search regulatory associations function allows the user to input a list of genes of interest and search for candidate transcription factors that regulate the list of genes. Allows filtering according to multiple criteria.

** The search regulatory associations function allows the user to input a list of genes of interest and search for candidate transcription factors that regulate the list of genes. Allows filtering according to multiple criteria.

** Allows user to input either a single transcription factor to get a list of regulated target genes or a single gene to get a list of transcription factors that regulate that gene. Can also filter according to a threshold value

** Allows user to input either a single transcription factor to get a list of regulated target genes or a single gene to get a list of transcription factors that regulate that gene. Can also filter according to a threshold value

** Downloaded the list of Cin5p targets with a threshold value >0.997.

** Downloaded the list of Cin5p targets with a threshold value >0.997.

** Multiple tools are provided on this server. Those of interest include a search for regulatory relationships either by transcription factor or by target gene. Applies a different algorithm to find new regulatory relationships in previously published data from Lee, Harbison, Tan and Workman

** Multiple tools are provided on this server. Those of interest include a search for regulatory relationships either by transcription factor or by target gene. Applies a different algorithm to find new regulatory relationships in previously published data from Lee, Harbison, Tan and Workman

*** One consolidated MAPP with Lee, Harbison, and Tan has been completed.

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** Workman et al.

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** Hu et al.

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** TVSM

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** Yeastract

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*** MAPPs for each of the above have been created as well.

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* Total compiled Cin5p target MAPP has also been created including all of the data above, saved on desktop in "Database and Reference TF Search" as Cin5Targets_Total_Compiled.mapp. Four total MAPPs were created because the max number of genes was exceeded.

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===Other Papers of Interest===

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*Cold Shock Temporal Network Data

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Used new algoithm to construct temporal networks of yeast's response to various stresses, including cold shock. For cold shock data, the paper analyzes data from the Gasch, ''et al.'' (2000) paper. Supplementary data has cold shock temporal response, but does not show any interactions between transcription factors and targets. (Note: the Gasch et al. paper does not have a true "cold shock" response. They only measure the effect of a temperature downshift from 37°C to 25°C. Cold shock is defined in the range of 10°C to 18°C''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 16:59, 22 September 2008 (EDT)'')

TF Network Data

//Updated TF network to determine new relationships
Used improved algorithms to detect new regulatory relationships in the transcription factor network
Fig. 3 Shows that the effect on Cin5 was to gain approximately 10 new interactions and lose approximately two as compared to the older model.
A figure of the new network was downloaded. PDF format

//Cold Shock Temporal Network Data
Used new algoithm to construct temporal networks of yeast's response to various stresses, including cold shock. For cold shock data, the paper analyzes data from the Gasch, et al. (2000) paper. Supplementary data has cold shock temporal response, but does not show any interactions between transcription factors and targets. (Note: the Gasch et al. paper does not have a true "cold shock" response. They only measure the effect of a temperature downshift from 37°C to 25°C. Cold shock is defined in the range of 10°C to 18°C

Web Servers

The search regulatory associations function allows the user to input a list of genes of interest and search for candidate transcription factors that regulate the list of genes. Allows filtering according to multiple criteria.

Allows user to input either a single transcription factor to get a list of regulated target genes or a single gene to get a list of transcription factors that regulate that gene. Can also filter according to a threshold value

Multiple tools are provided on this server. Those of interest include a search for regulatory relationships either by transcription factor or by target gene. Applies a different algorithm to find new regulatory relationships in previously published data from Lee, Harbison, Tan and Workman